Thats fine. This question still remains, "As for the rest, did you resign your macros? You can do this in the System app under Macros>Signatures. Just resign them all as it will use the new Key vs. the database connection string."

To clarify the issue I followed up with my dev team and the upgrade is more complex than I was told. The client is going from 6.04 > 7 > 8 > 9.

So to test when the issue began, and to be clear that all the steps where followed, I began the process again. I applied the first update using the updater (Not Manual). The updater ran without any errors, but we had written some custom code that needed to have some minor changes based on the library changes in 7.

After this was done I ran the site and noticed that I am getting a 404 when images are called from the images.zip file in the Theme directory.

I have look into the following and it has not helped.
http://devnet.kentico.com/questions/missing-images-and-images-zip-archive

Below are the two links for comparison as well as the error that I am getting. As you can see the "Add To Cart" image loads from the 6.0.4 version but not the 7 version. Also the Shopping cart images cannot be found. This looks like an issue finding the zip file.

Have you checked your web.config file for the runAllManagedModulesForAllRequests variable? Sometimes the upgrade will wipe that out, it that's not under the system. That could be messing up some images...Also maybe compare your file structure with a new 9 instance and see if there are differences. If there are, you can either try to copy your application files over to the new 9 instance and test it, or maybe get a sense of what extra files or files you are missing.